Wednesday, March 31, 2010

Cornelius Hunter blogs at Darwin's God. He has a Ph.D. in Biophysics and Computational Biology and currently teaches at Biola University. He is a Fellow of the Discovery Institute and the author of several books that I have not read.

Hunter has devoted most of his blogging efforts to attacks on science. This seems to be the most popular strategy of the Intelligent Design Creationists in spite of their claims to the contrary.

Evolutionists say evolution is a fact, every bit as much as gravity is a fact. That is remarkable. We see and even feel gravity everyday. Evolution, on the other hand, entails rather dramatic, one-time, events that were supposed to have occurred long ago, when no one was around to witness them. How could we be sure of such a theory? There must be some extremely powerful and compelling scientific evidence for evolution to make it a fact as gravity is a fact. That is what one would think. But, surprisingly, there is no such evidence. When evolutionists try to explain why evolution is a fact, it is a tremendous anticlimax.

Hunter has not been paying attention. Many of us have written on the subject of evolution as a fact [Evolution Is a Fact and a Theory]. Evidence for the "factness" of evolution is overwhelming. It ranges from evidence that chimps and humans descend from a common ancestor to evidence that the frequencies of alleles are changing in populations as we speak.

That last point is important. Evolution is defined as a change in the frequency of alleles in a population over time and as long as we can demonstrate that change, the fact of evolution can't be disputed. I wonder how Cornelius Hunter explains the differences between the Japanese and the Masai of Kenya and Tanzania? I wonder how he explains the fact that native North Americans are practically homogeneous for O blood type? I wonder how he explains the many studies that have directly tracked heritable change over many generations?

Why are the IDiots so stubborn and so ignorant? Why couldn't Cornelius Hunter demonstrate that he understands why evolution is a fact while disputing some forms of macroevolution? That would be a sensible position. Instead, he comes off looking like an IDiot.

Tuesday, March 30, 2010

This is the second in a series of postings by a guest blogger, Arlin Stoltzfus. You can read the first part at: Introduction to "The Curious Disconnect". Arlin is challenging the status quo in modern evolutionary theory. He's not alone in this challenge but it's important to distinguish between kooks who don't know what they're talking about and serious thinkers who have something to say. Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. I'm happy to give him a chance to post on Sandwalk.

The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored.Our journey to explore The Curious Disconnect-- the gap between how we think about evolution and how we might think if we were freed from historical baggage-- begins with the Mutationism Myth. In this, the first of four parts, we are not going to confront any tough scientific or conceptual issues. Instead, we are just going to review an odd story about our intellectual history.

The Mutationism Story

While "myth" has the connotation of falsehood, the story that a myth tells isn't necessarily a false one. The mutationism myth, at least, is anchored in historical events.1

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored. The villains of the story are the influential early geneticists or "Mendelians" who saw genetics as a refutation of Darwinism; the heroes are first, the founders of population genetics, theoreticians who sorted everything out in favor of Darwinism by about 1930, and second, the architects of the Modern Synthesis, activists who popularized and institutionalized what we're calling "Darwinism 2.0".

This story has been re-told in secondary sources for nearly 50 years, though I sense that the frequency is decreasing as this episode passes into ancient history. To find examples, try looking up "mutationism" (sometimes "Mendelism" or even "saltationism") in the index of a book about evolution.

I encourage you to consult whatever sources you have and to share the stories that you find. Note that you won't always be successful. A quick survey of several dozen contemporary books on my shelf reveals that most don't address this episode specifically (a notable absence, in some cases 2); some tell the mutationism myth with varying degrees of panache; and a few provide a historical account rather than a myth. The few historical accounts that I found were in Gould's 2002 The Structure of Evolutionary Theory, Strickberger's 1990 textbook Evolution, and the Wikipedia entry on "Mutationism".

Sample stories

Lets look at a few examples of the mutationism story. Readers who want to check out a freely available online source from the scholarly literature may refer to Ayala and Fitch, 1997 (http://www.ncbi.nlm.nih.gov/pubmed/9223250?dopt=Citation). One example that really caught my eye is not from scientific literature, but from the 2005 obituary for Ernst Mayr in The Economist:

It was not that biologists had given up on evolution by the 1940s-quite the contrary. But they had got very confused about its mechanism. . . . The geneticists of the early 20th century did not help. They rediscovered the laws of inheritance first developed 40 years earlier by Gregor Mendel, an unsung Moravian monk. They also discovered the idea of genetic mutation. But instead of linking these things to natural selection, they came up with the idea of "saltation"-in other words, sudden mutational shifts from one well-adapted species to another. Nor, the geneticists complained, had there been enough time for natural selection to do its work, given what they had discovered about the rate at which mutations occur, and the fact that most mutations are deleterious. It was all a bit of a mess. . .Mr Mayr's advantage over the laboratory-bound biologists who had hijacked and diluted Darwin's legacy was that, like Darwin, he was a naturalist-and a good one. (anonymous, 2005)

Of course, this is a magazine article, written by anonymous staff writers-- typically one doesn't see such florid language in the scholarly literature. But did the staff writers of the Economist (representing elite opinion) really originate this story, based on their own personal recollections of the 1930's? Of course not. Mayr himself popularized the image of geneticists as laboratory-bound geeks lacking the organic insight of "naturalists". This disdain for the geneticists who "hijacked" Darwin's legacy is readily apparent when evolutionary writers depict geneticists as fools holding "beliefs" that have "obvious inadequacies", unable to understand or "grasp" their own scientific findings:

"It is hard for us to comprehend but, in the early years of this century when the phenomenon of mutation was first named, it was regarded not as a necessary part of Darwinian theory but as an alternative theory of evolution! There was a school of geneticists called the mutationists, which included such famous names as Hugo de Vries and William Bateson among the early rediscoverers of Mendel's principles of heredity, Wilhelm Johannsen the inventor of the word gene, and Thomas Hunt Morgan the father of the chromosome theory of heredity. . . Mendelian genetics was thought of, not as the central plank of Darwinism that it is today, but as antithetical to Darwinism. . . It is extremely hard for the modern mind to respond to this idea with anything but mirth" (Dawkins, 1987, p. 305)

"According to mutationism, random changes in the hereditary material are sufficient for adaptation without much, or any, selection at all. Mutations just somehow happen to be adaptive, the right changes simply manage to occur. The inadequacies of this view are obvious" (Cronin, 1991, p. 47).

"Darwin knew nothing of this [i.e., genetics] but as it turned out, his ignorance was sublimely irrelevant to the problem he was really interested in tackling: evolution. This point was not fully grasped by biologists. Many early geneticists at the dawn of the 20th century, thought their discoveries of the fundamental principles of genetics somehow cast doubt [on], or rendered obsolete, the concept of natural selection. It took several decades of experimentation and theoretical (including mathematical) analysis to show not only that there was no conflict inherent between the emerging results of genetics and the older Darwinian notion of natural selection, but that the two operate in different domains." (Eldredge, 2001, p. 67)

"Mendelian particulate inheritance (today, we call the "particles" genes) was originally identified with De Vries's "mutation theory", according to which new variations or species originated in large jumps, or macromutations, and evolution was exclusively explained by mutation pressure. Darwinian naturalists, believing that Mendelism was synonymous with mutation theory, held on to theories of soft inheritance, while they considered selection a weak force at best. They did not know of the new findings in genetics that would have supported Darwinism. (SegerstrŒle, 2002)

Notice how, in every version of the story above, the position taken by early geneticists just doesn't make sense. This isn't a story of theory versus theory, its a story of confusion ultimately yielding to reason.

If de Vries and the other geneticists are playing the role of the pied piper in this story, the "naturalists" are like the children lured away from their Darwinian home. Ultimately the innocents are returned, and order restored, by (oddly enough) mathematicians:

"Between 1918 and 1932 Fisher, Haldane, and Wright showed that Mendelian genetics is consistent with natural selection. Only then, more than 60 years after the publication of The Origin of Species, was the genetic objection to natural selection finally removed. Modern molecular and developmental genetics have confirmed in exquisite chemical detail the key aspects of genetics necessary for Darwin's ideas to work: that the genetic material is DNA, that DNA has a sequence, . . . mutates . . . contains information . . " (p. 16 of Stearns and Hoekstra, 2005)

Anatomy of a Myth

In a subsequent post, we will look at original sources to see what the "mutationists" actually believed, and why. And eventually we will integrate this into the bigger picture of how evolutionary theory developed. But for now, lets just summarize the pattern that is apparent in the literature.

First, the mutationism story is clearly a story or myth, and not an ordinary scientific truth claim. We can see this because the story-tellers are not using ordinary scientific conventions to convince us that the story is true. If you or I were making an ordinary scientific argument (for instance) for an effect of "translational selection" on codon usage, we would mention a correlation between codon frequencies and the abundance of corresponding tRNAs, citing the classic work of Ikemura (1981), and we might even repeat a figure showing this correlation, to impress this point upon the minds of readers (e.g., just as in Ch. 7 of Freeman & Herron, 1998).

When I see instances of the mutationism story, typically I don't find quotations illustrating what the mutationists believed, nor facts & figures to refute their views, but only vague attributions and generalized claims. Apropos, the following quotation from Ernst Mayr never fails to make me laugh:

The genetic work of the last four decades has refuted mutationism (saltationism) so thoroughly that it is not necessary to repeat once more all the genetic evidence against it. (Mayr, 1960)

And the puissant Dr. Mayr proceeds on, not boring the reader with any tiresome "genetic evidence", nor citing sources that might allow the reader to evaluate the truth of his statement. Its a story, after all.

By contrast, the 3 sources that I mentioned above as providing scientific history, rather than myth, all make reference to specific experimental and theoretical results, and reveal knowledge of specific historically important scientific works. For instance, Strickberger's reference list includes Johannsen, 1903, as well as the 1902 paper by Yule that reconciled Mendelian genetics with quantitative variation (in neo-Darwinian mythology, credit for Yule's work is given to little Ronny Fisher, who was 11 at the time).

Second, every story has a plot or "action", and the main action of the mutationism story is a turn of fate in which power is temporarily in the hands of the wrong people or ideas. In archetypal terms, its a story of usurpation and restoration: the throne is usurped, and the kingdom falls into darkness and confusion until the throne is restored to the king's rightful heirs. The mutationism episode didn't have to be told that way: it might have been presented as a period of reform (in which old ideas were abandoned) or discovery (when new territory was mapped out). Instead, its presented as a mistake, an interlude of confusion, a collective delusion.

Indeed, another way to look at the mythic action is that the Mendelians are wizards or false prophets who place the kingdom under a spell, leading folks astray and causing them to believe things that they just shouldn't have believed.

What delusional spell did the Mendelians cast? In the story by Eldredge, or by Stearns & Hoekstra above, the spell is that Mendelian genetics is inconsistent with "the concept of natural selection" (Eldredge). In the story told by SegerstrŒle, Cronin, Mayr and The Economist, the delusional spell is a bit different: the principle of selection is irrelevant because mutational jumps alone explain evolution.

Third, the key to restoring Darwin's kingdom was to add themissing piece of genetics. Ultimately, after the period of darkness ended, the discovery of genetics "provided the missing link in Darwin's theory" (SegerstrŒle, 2002), or "The missing link in Darwin's argument was provided by Mendelian genetics" (Ayala & Fitch, 1997). Darwinism was restored, not by taking away the power of genetics, but by redirecting it to support Darwinism. Clearly, genetics is the key to ruling the kingdom, like the One Ring that Rules them All in Tolkien's world. The ones who have the ring have the power.

The story is made more fascinating by the fact that the key to power is literally a code of rules developed by a monk that remained lost for nearly half a century. The usurpers who discover The Monk's Code misinterpret it, and use it to overthrow the true king, establishing a reign of error. But when The Founders decipher the true meaning of the Monk's Code, The Architects campaign throughout the kingdom, spreading the news: the Monk's Code proves that Darwin is the true king. Darwin's rule is re-established, all opposition ceases, and the kingdom is unified.

Homework

If you would like to contribute a mutationism story, I would be happy to start a collection if you make it easy for me by providing a complete and well formed text item. Be sure to provide a quoted passage with a source, citing exact page numbers. If we get enough stories, lets try to recruit a sociologist or historian to study this further.

Summary

To summarize, the mutationism story is a myth that is retold in secondary sources. The basic story is simple: the discoverers of genetics misinterpreted their discovery, thinking it incompatible with Darwinism; Darwinism went into disfavor; population geneticists came along and showed that genetics was the missing key to Darwinism; Darwinism was restored and once again reigned supreme.

For now, note how the writers quoted above are genuinely baffled by our scientific history. It just doesn't make sense to them. A century ago, most of an entire generation of scientists thought of genetics as a contradiction of Darwinism. This is a historical fact, and presumably it has an explanation that rational folks can understand by examining what scientists of the time wrote. But this historical fact mystifies Dawkins, Eldredge, Cronin, and others.

Ikemura, T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389-409.

Mayr, E. 1960. The Emergence of Evolutionary Novelties. Pp. 349-380 in S. Tax, and C. Callender, eds. Evolution After Darwin: The University of Chicago Centennial. University of Chicago Press, Chicago.

Notes1The defining characteristic of a myth is not that it isn't literally true, but that it isn't told for reason of being literally true, but for reason of being meaningful or poignant: a myth is a story with a cultural value, not necessarily a literal-truth value. The connection between myths and untruths, then, has to do with discoverability: when we find a pattern P = { X people are repeating story Y }, where X is a large number, this pattern by itself does not prove that Y is a myth because X people might have all discovered or verified Y independently; but if Y has diverse elements that are untrue (or unverifiable), then we can conclude that its repetition does not signify independent verification, suggesting that its a myth.

2The Oxford Encyclopedia of Evolution does not have an article on mutationism; the article on Morgan says nothing of his views on evolution; there is no article on Bateson; mutationism is only addressed peripherally in Hull's article on the history of evolutionary theory; it is mainly addressed in SegerstrŒle's article on neo-Darwinism.

Sunday, March 28, 2010

Paul Nelson is a Young Earth Creationist. He believes the Earth is less than 10,000 years old and all modern species were created separately. Nelson is also a Fellow of the Discovery Institute. Given these two facts you might wonder if anything he says is worth listening to. The answer is "yes"—lots of his writings are very (unintentionally) amusing.

Paul Nelson's latest posting on Uncommon Dissent falls into a different category. It ain't particularly funny but it does perpetuate a false impression that's very common among the IDiots, and, unfortunately, some others who should know better.

What has changed within the past couple of years, however, is the rapid growth in the overtly religious (anti-religious, but that anti doesn’t really matter) content of the writings of prominent neo-Darwinian biologists, such as Jerry Coyne and Richard Dawkins. The Accomodationist Wars, which show no signs of slacking, illustrate that for many, the whole point of evolutionary theory is Getting Rid of God. A biologist who nonetheless professes his theism (Ken Miller, Simon Conway Morris, Francis Collins, et al.) — well, those people are, at best, confused. Evolution properly understood is irreligious. Not “irreligious” in the sense of indifferent or neutral. Hostile. Read the traffic at Pharyngula, Why Evolution is True, Dawkins’s site, Sandwalk, or dozens of other blogs and discussion boards. [Just to be clear: I (PN) don't think the theory of evolution is irreligious, in the sense of hostile to theism. Philosophical naturalism, however, is. But evolution and naturalism are typically conflated by their advocates.]

The accommodationist wars are about the conflict between science and religion and not "evolutionary theory" and religion. People like Paul Nelson would like to change the topic because they want to be seen as anti-evolution but not necessarily anti-science.

And it's not just "neo-Darwinians"1 who declare that science and religion are incompatible. All kinds of scientists share this opinion. For example, there are more than a few astronomers and geologists who think the Earth is slightly more than 10,000 years old. They are firmly convinced that science is totally incompatible with Young Earth Creationism.

I guess Paul Nelson doesn't know that.

He also doesn't know that the big battle is between rationalism and superstition. In this fight atheists are trying to convince theists that their gods are delusions and they should abandon them. Some of these atheists are scientists but many are not. Don't confuse the two fights. "Science vs. religion" overlaps with "rationalism vs. superstition" but "evolution vs. creationism" is often a very separate battle. People like Ken Miller can be mostly with the good guys in "evolution vs creationism" while being on the wrong side of "rationalism vs superstition."

La Presse is a large circulation daily newspaper in Montreal (Canada). Today's issue has front page coverage of the "battle" between real doctors and phoney ones. Coverage begins on the front page with "Herbs or Vaccines?" [Médecine: des herbes ou une piqûre?].

The collection of articles inside presents a very favorable case for non-evidence based medicine (i.e. alternative medicine), although it does toss a few bones toward skepticism by quoting some "traditional" doctors (i.e. doctors who rely on evidence in making decisions about the well-being of their patients).

This is "science" reporting at its worst. The lead reporter is Pascal Breton who graduated form l'Université du Québec à Montréal with a degree in journalism, She used to write about provincial politics but she has been covering health issues at La Presse for the past four years.

Thursday, March 25, 2010

As most of us know, the Templeton Prize goes to, "outstanding individuals who have devoted their talents to expanding our vision of human purpose and ultimate reality. The Prize celebrates no particular faith tradition or notion of God, but rather the quest for progress in humanity’s efforts to comprehend the many and diverse manifestations of the Divine." In other words, it's a prize of £1,000,000 sterling for the best accommodationist. The National Center for Science Education has just posted an official press release praising the winner of this religious prize [Ayala wins the Templeton Prize.]

What's up with that? What does tying to understand God have to do with science education? I don't know if NCSE makes a habit of issuing press releases for this sort of thing. Does anyone know if they've posted official press releases for the winners of the Richard Dawkins Award given out by Atheist Alliance International?

In case there was ever any doubt, NCSE publicity supports the position that science and religion are compatible.

Here's the full press release ...

NCSE congratulates Francisco J. Ayala on winning the Templeton Prize. The prize, worth about $1.5 million, is awarded annually by the John Templeton Foundation to "a living person who has made exceptional contributions to affirming life's spiritual dimension." A March 25, 2010, press release from the Foundation highlighted Ayala's vigorous opposition to "the entanglement of science and religion while also calling for mutual respect between the two," saying, "Even as he has warned against religion’s intrusion into science, Ayala, a former Dominican priest, also champions faith as a unique and important window to understanding matters of purpose, values and the meaning of life." Ayala told the Los Angeles Times (March 25, 2010) that he regarded the award as honoring his scientific work and its "very important consequence of making people accept science, and making people accept evolution in particular."

In his essay "Science and religion: Conflict or dialogue?" posted on the Washington Post's On Faith blog (March 25, 2010), Ayala sketched his views on science and religion, writing, "Science and religious beliefs need not be in contradiction. If they are properly understood, they cannot be in contradiction, because science and religion concern different matters. ... The proper relationship between science and religion can be, for people of faith, mutually motivating and inspiring. ... As I see it, scientific knowledge is consistent with a religious belief in God. More so than the 'creationists[']' assertion that everything in the world has been precisely designed by the Creator. Because, then, how to account for human crimes and sins (including the Biblical Fall) and for all the catastrophes that pervade the natural world?" His Darwin's Gift to Science and Religion (Joseph Henry Press, 2009) presents his views in greater detail.

A Supporter of NCSE since its founding, Ayala is University Professor, the Donald Bren Professor of Biological Sciences, and Professor of Philosophy at the University of California, Irvine; he received the National Medal for Science, the nation's highest award for lifetime achievement in scientific research, in 2002. Among his contributions to the defense of the integrity of science education was his testimony for the plaintiffs in McLean v. Arkansas and his coordination of support for evolution education at the National Academy of Sciences, including his lead authorship of the publication Science, Evolution, and Creationism (National Academies Press, 2008). NCSE's executive director Eugenie C. Scott commented, "Ayala's contributions to NCSE and its goal of defending the teaching of evolution in the public schools are comparable to his contributions to biology in general: immense."

Francisco Ayala has won this year's Templeton Prize. It's a very wise political choice on the part of the Templeton Foundation since Ayala is a top notch evolutionary biologist and a vocal opponent of Intelligent Design Creationism.

The announcement was made at the National Academy of Sciences in Washington D.C. A few year ago, Ayala chaired the committee that product the NAS booklet on Science, Evolution, and Creationism. That book made the case for science and it also made the case for accommodationism—something that NAS should have avoided.

Here's a repeat of a posting I made on January 4, 2008. It explains why science organizations get into trouble when they try to support some religions and not others. They should be neutral.

The National Academies (Science, Engineering, Medicine) (USA) have just published their latest book on the evolution/creationism controversy. You can download it for free on their website [Science, Evolution and Creationism].

Like the previous versions, this one is quite well done. It explains evolutionary concepts correctly and gives clear examples of the evidence supporting the fact of evolution. The book—actually a large pamphlet—describes the various forms of creationism and why they are rejected by science.

I was troubled by one part of the book describing the compatibility of science and religion. It's only two paragraphs plus three pages of quotations but it promotes the fallacy of the Doctrine of Joint Belief. This fallacy makes a virtue out of compartmentalization. It says that because scientist X is religious, it follows that religion and science are compatible. Similarly, because religious leader Y, accepts evolution, it follows that science and religion are not in conflict.

But this volume is unusual, people who worked on it say, because it is intended specifically for the lay public and because it devotes much of its space to explaining the differences between science and religion, and asserting that acceptance of evolution does not require abandoning belief in God.

...

The 70-page book, “Science, Evolution and Creationism,” says, among other things, that “attempts to pit science and religion against each other create controversy where none needs to exist.” And it offers statements from several eminent biologists and members of the clergy to support the view.

I think it's unfortunate that the New York Times article places so much emphasis on this part of the book but the authors of the book1 must have known what they were doing. Too bad they were misguided.

Here's what they wrote in Science, Evolution and Creationism,

Acceptance of the evidence for evolutioncan be compatible with religious faith.

Today, many religious denominations accept that biological evolution has produced the diversity of living things over billions of years of Earth’s history. Many have issued statements observing that evolution and the tenets of their faiths are compatible. Scientists and theologians have written eloquently about their awe and wonder at the history of the universe and of life on this planet, explaining that they see no conflict between their faith in God and the evidence for evolution. Religious denominations that do not accept the occurrence of evolution tend to be those that believe in strictly literal interpretations of religious texts.

Science and religion are based on different aspects of human experience. In science, explanations must be based on evidence drawn from examining the natural world. Scientifically based observations or experiments that conflict with an explanation eventually must lead to modification or even abandonment of that explanation. Religious faith, in contrast, does not depend only on empirical evidence, is not necessarily modified in the face of conflicting evidence, and typically involves supernatural forces or entities. Because they are not a part of nature, supernatural entities cannot be investigated by science. In this sense, science and religion are separate and address aspects of human understanding in different ways. Attempts to pit science and religion against each other create controversy where none needs to exist.

There are two fallacies here. The first one is the one I already alluded to (the Doctrine of Joint Belief). Just because you can find scientists and theologians who proclaim that evolution is compatible with religious faith doesn't make it so. You need to examine their understanding of evolution and also what they mean by "religious faith."

As you might have guessed, the book trots out quotations from the usual suspects, Francis Collins and Kenneth Miller2. Their words of wisdom appear on a page with the title "Excerpts of Statements by Scientists Who See No Conflict Between Their Faith and Science." The book makes some amends, in my opinion, by including the following statement on that page.

Scientists, like people in other professions, hold a wide range of positions about religion and the role of supernatural forces or entities in the universe. Some adhere to a position known as scientism, which holds that the methods of science alone are sufficient for discovering everything there is to know about the universe. Others ascribe to an idea known as deism, which posits that God created all things and set the universe in motion but no longer actively directs physical phenomena. Others are theists, who believe that God actively intervenes in the world. Many scientists who believe in God, either as a prime mover or as an active force in the universe, have written eloquently about their beliefs.

The good part about that statement is that it mentions deism, which is a form of religion where the conflict between science and religion really is minimized. The bad parts are that theists who promote interventionist Gods are touted as examples of those who see no conflict between science and religion. (The reason why Theistic Evolutionists don't "see" a conflict is because they choose to look the other way [Theistic Evolution: The Fallacy of the Middle Ground].)

The other bad part is that atheists are equated with the philosophical position of scientism. That's an unnecessary complication. It would have been sufficient, and preferable, to state that many scientists do not believe in supernatural beings. They could have gone on to state that many of those non-believers see a conflict between science and the supernatural.

The second fallacy in the two paragraphs quoted above is something I call the Fallacy of the Undetectable Supernatural. The authors of Science, Evolution and Creationism repeat the silly argument that "supernatural entities cannot be investigated by science." Why not? The only kind of supernatural beings that could never be investigated by science are those that exist entirely as figments of the imagination and have absolutely no effect on the real world as we know it. As soon as your God intervenes in the real world his actions become amenable to scientific investigation.

In this, I agree with Stephen Jay Gould's description of Non-Overlapping Magisteria (NOMA). He states very clearly that religion violates NOMA as soon as it makes a claim for an interventionist God (Gould, 1999). In that case religion is no longer compatible with science.

The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.

Stephen Jay Gould (1999) pp. 85-85

The National Academies are violating NOMA unless they specifically refer to belief in Gods that do not perform miracles of any kind. There are very few religions that believe in non-interventionist Gods who never perform miracles. Therefore, it is much more scientifically accurate to say that science conflicts directly with almost all religious beliefs, including those of Ken Miller and Francis Collins.

This is an important error in Science, Evolution and Creationism since Americans have a right to expect that the National Academies can define the proper magisterium of science. Instead, the National Academies, like NCSE, has taken the easy way out by redefining science as that field of study that is not in conflict with the religious views of Francis Collins and Ken Miller.

1. The books was produced by a committee headed by Fancisco Ayala.

2. Who appointed Collins and Miller to be the flame carriers for evolution?

Gould, S.J. (1999)Rock of Ages: Science and Religion in the fullness of Life The Ballantine Publishing Group, New York (USA).

Tuesday, March 23, 2010

The American National Academy of Science has agreed to serve as the host for the Templeton Foundation as they give out a prize to the best person who speaks in favor of science and religion. (Francis Collins is the odds-on favorite to win.) This is despicable behavior for a "scientific" organization. Why can't they be neutral when it comes to the potential compatibility science and religion?

How many of you think the National Academy would host an award for the best atheist scientist?

Previous Templeton Prize winners include: Mother Theresa, Billy Graham, Aleksandr Solzhenitsyn, Chuck Colson and Freeman Dyson. Only one of these was eligible for membership in the National Academy of Science.

Sunday, March 21, 2010

As most of you know, chiropractors in the UK are coming under the gun for making false, unscientific claims. This backlash was prompted by a suit launched by the British Chiropractic Association against Simon Singh. Singh's "crime"?—he suggested in an newspaper article that many claims by chiropractors were bogus.

The regulations governing chiropractors in North America are much more lax than those in the UK. Canadian and American chiropractors can make all sorts of claims about their treatment—claims that have no scientific evidence to support them—without incurring any penalties. Whereas British chiropractor websites have been take down for fear of prosecution, those in North America are still going strong.

Saturday, March 20, 2010

Michael Ruse has published some articles on The BioLogos Foundation website. Recall that this foundation was set up by Francis Collins and its mission is very clear.

The BioLogos Foundation is a group of Christians, many of whom are professional scientists, biblical scholars, philosophers, theologians, pastors, and educators, who are concerned about the long history of disharmony between the findings of science and large sectors of the Christian faith. We believe that the Bible is the inspired Word of God. We also believe that evolution, properly understood, best describes God’s work of creation. Founded by Dr. Francis Collins, BioLogos addresses the escalating culture war between science and faith, promoting dialog and exploring the harmony between the two. We are committed to helping the church – and students, in particular – develop worldviews that embrace both of these complex belief structures, and that allow science and faith to co-exist peacefully.

BioLogos represents the harmony of science and faith. It addresses the central themes of science and religion and emphasizes the compatibility of Christian faith with scientific discoveries about the origins of the universe and life. To communicate this message to the general public and add to the ongoing dialog, The BioLogos Foundation created BioLogos.org.

Got it? This is a group of people who think that science and religion (e.g. evangelical Christianity, Roman Catholicism) are compatible with science.

And yet, I am excoriated at every turn. Why? Simply, because I am an “Accommodationist.” I think that some kind of intellectual meeting is possible with religious believers, including Christian religious believers. As it happens, I believe that in America it is tremendously important politically to bring evolutionists together with people of religious commitment, but I absolutely and completely would not argue for a position that I thought wrong because it was politically expedient to do so. I would not say that emotion plays no role in my position. It does indeed. That helps me to take a stand that I think right against folk with whom I would much rather be a friend than a scorned enemy. But I think one can make a sound case for the position I have taken and still accept strongly today. In this essay, I try to explain what I believe and why I believe it. Why I am an “Accommodationist,” whatever that might mean, and proud of it.

Please understand: this piece I am writing now is not so much a response as a reaction. What I mean by this is that I don’t want to whine about being mistreated or misunderstood or whatever. As I have already intimated, in a way to respond in such a way would be almost hypocritical, because I rather like the fact that I stir people up so much that they want to strike out as they do. But I think there is some value in trying to see where I have come from, what I believe at the moment, and why I have fallen out (or raised the ire of, because frankly it was not I who started the quarrel) of people who in most respects you would think would be my natural allies. I am going to write this in a rather personal way because above all it is rather personal. I think, however, even those of you who think writers should never reveal anything of themselves will be able to strain through the personal and see the arguments underneath.

Oh dear! Ruse is terribly confused.

The accommodationist term was made up to describe atheists who go out of their way to defend religious beliefs as being compatible with science.1 They claim that religion is a way of knowing separate from science. They claim that science can't investigate the important claim of religion so it's perfectly okay to be a scientist and, at the same time, believe in life after death, miracles, and humans who are the son of God. They are accommodationsts because they pretend there's no conflict between science and many religious beliefs.

Accommodationists are NOT defined as people who have Christian friends and who are willing to ally with their friends on common causes like keeping creationism out of the schools. Those are traits shared by those of us who believe that science and religion are incompatible. Believe it or not, I have friends who believe in God and so does PZ Myers and Richard Dawkins. (I suspect Jerry Coyne probably has such friends as well.) Bringing that up only confuses the issue.

I can't believe that Ruse is ignorant of this distinction because he's written many articles about the compatibility of science and religion. Is he being deliberately misleading on the BioLogos website?

Perhaps he'll clarify this point and demonstrate that he understands the difference between being an accommodationist and being a friend and ally of people who believe in the supernatural. There are going to be more essays, but you can skip Part II [Accommodationist and Proud of It, Part II: A Christian Childhood]. There's nothing worth reading there.

P.S. Michael Ruse complains a lot about being misunderstood. The remedy is not to blame his opponents—although we are rarely blameless—but to try and write more clearly.

1. They were originally called Neville Chamberlain Evolutionists, as Ruse points out in his article. That term has been dropped but you get the idea. Accommodationists describe otherwise intelligent atheists/evolutionists who compromise their principles when it comes to dealing with the beliefs of some (but not all) believers. They do this in order to maintain the peace.

Given what we know about errors in DNA replication, we estimate that every human infant carries 130 new mutations [Mutation Rates].

This number correspond to 75 mutations per haploid genome per generation or a mutation rate of 2.3 × 10-8 per base pairs in the haploid genome (3.2 × 109) per generation. This value is consistent with a variety of experimental measurements, notably the rate in Y chromosomes [Human Y Chromosome Mutation Rates].

A recent paper in Science attempted a direct measurement of the mutation rate by comparing the complete genome sequences of two offspring and their parents. They estimate that each offspring had 70 new mutations (instead of the predicted 130) for a mutation rate of 1.1 × 10-8 per haploid genome per generation (Roach et al. 2010).

This value is only half of the rate expected from previous results and John Hawks is pretty concerned about that: A low human mutation rate may throw everything out of whack. If it's true then the time of divergence of humans and chimps would have to be set at 9 Myr and a lot of studies of recent human evolution could be off by a factor of 2.

I don't think there's any cause for concern because the measured rate in these sequenced genomes is not nearly as reliable as you might think. Most people imagine that it's merely a question of adding up all the differences between the genomes of the two offspring and their parents. Problem is, that number came to 49,720 potential mutations and that's certainly wrong. What to do?

The authors checked their data and did a bunch of re-sequencing to confirm the differences. They ended up with 28 confirmed differences in the two genomes. That's too low, so they went back over the data to see if they could find false negatives. After some careful analysis they were able to estimate the false negative rate and adjust the final tally to 70 new mutations in each diploid offspring. (Recall that the calculation based on known DNA replication error rates was 130 mutations per diploid genome per generation.)

This is how they arrived at their final value of a mutation rate. Given the possible sources of error in the genome sequence data, I don't think we should get too excited about this number. After all, it's only a bit lower than previous estimates. We should be celebrating the remarkable consistency of the data and not the variability.

John, you don't need to re-write your grant—at least not for that reason.

This is the first of a series of postings by a guest blogger, Arlin Stoltzfus. Arlin has some important ideas about modern evolutionary theory and I'm happy to give him a chance to put them on Sandwalk.

Arlin Stoltzfus is a computational biologist with a background in bacterial population genetics and molecular evolution. He is a Research Biologist at the National Institute of Standards and Technology (NIST), and a Fellow of the Center for Advanced Research in Biotechnology. Much of his current work focuses on software and databases for evolutionary analysis, in collaboration with an international group of peers interested in improving interoperability. He also does basic research on evolution, and has contributed to our understanding of the history of introns, the origins of complexity, and the role of mutation in evolution. When he isn't doing science or spending time with family, his favorite diversions are playing the piano, bicycling, and martial arts.

This is a longish introduction to a series of postings that will be released over the next 6 months or so. A version of this document with corrections and updated links will be maintained at http://www.molevol.org/files/cdblog/intro.html.

Striking a chord

The title of this series—The Curious Disconnect—comes from a 2002 article by eminent evolutionary geneticist Allen Orr (Orr 2002), who had broken new ground by developing predictive models of adaptation, and was reflecting on why such models weren't developed long ago, referring to "a curious disconnect between the verbal theory that sits at the heart of neo-Darwinism and the mathematical content of most evolutionary genetics".

That struck a chord with me. Since the 1990s, I had struggled with a "disconnect" that emerged while I was digesting a think-piece by paleontologists Elisabeth Vrba and Niles Eldredge (Vrba and Eldredge 1984). Among other things, Vrba & Eldredge made the startling suggestion that a key theme of "evo-devo" was that "bias in the introduction of phenotypic variation may be more important to directional phenotypic evolution than sorting by selection". By 1999 when Constructive Neutral Evolution appeared (Stoltfus 1999), my thinking had shifted noticeably toward emphasizing 1) the mechanistic distinction between the process of introducing variants and the (separate, subsequent) process of reproductive sorting (selection and drift), and 2) a research program of accounting for non-randomness (in evolution) by invoking both bias in the introduction process, and bias in the sorting process.

This way of thinking suggested that mutational-developmental bias in the introduction of variation was a general cause of evolutionary bias or direction. That contradicted two things I knew about evolutionary thinking. First, I knew that the notion of "internal" variational causes of direction, called "orthogenesis", had been rejected as a heresy. Second, I knew that, among contemporary researchers, mutation bias was not seen as a general bias on the course of evolution, but as a special aspect of neutral evolution, incompatible with selection.

I was confident that Vrba & Eldredge were headed in the right direction, but when I surveyed the theoretical literature, I could not find proof. Instead, Fisher, Haldane and Wright—the canonical founders of theoretical population genetics—all argued against a causal link between mutation and the direction of evolution, on the grounds that "mutation pressure" would be overcome by opposing "selection pressure", as in their mutation-selection balance models. Later, when "neutral" thinking became popular, this "opposing pressures" schema was interpreted to mean that mutation-biased evolution is possible, but only when selection "pressure" is absent. This was the conventional wisdom, but I knew it was wrong.

Thus, a few years later, when Lev Yampolsky and I (2001) used computer simulations to demonstrate that bias (mutational or developmental) in the introduction of variation is a possible cause of direction in neutral or adaptive evolution, we were showing a causal link that is both 1) a basic principle of population genetics, and 2) a heresy at odds with the professed views of the founders of population genetics.

What a "disconnect"! Indeed, the first premise of this blog series is that the "disconnects" in evolutionary biology are not just curiosities, but important challenges.

Deeper into the "disconnect"

Eventually I came to see these two "disconnects" as parts of the same syndrome. The retarded development of what Orr sees as predictive models of "Darwinian adaptation" is due mainly to the fact that the models are not properly Darwinian. These models (like many used in molecular evolution) treat evolutionary change as a recurring origin-fixation process in which new mutant alleles are introduced, and then individually face acceptance or rejection according to a probability function representing the effect of reproductive sorting.1 Our Darwinian ancestors rejected this kind of "lucky mutant" or "mutationist" framework as anti-Darwinian.

Instead, they were committed to a view in which adaptation takes place at many loci simultaneously on the basis of infinitesimal variation so abundant that the process does not depend on the rate of new mutations. Given such a view, "evolution" can be reduced to shifting the frequencies of alleles already in the "gene pool". When evolution is redefined in this way, the introduction process disappears and its effects become inaccessible. This explains the retarded development of the Yampolsky-Stoltzfus model.

Notice that this is not just a matter of "verbal theory" versus "mathematical content". Vrba & Eldredge had a verbal theory that suggested a way to combine causes, and Yampolsky & Stoltzfus demonstrated its implications formally with computer simulations; Wright, Haldane and Fisher had a verbal theory of combining causes that drew on mathematical treatments of mutation-selection balance. These two conceptions of evolution lead to two different predictions on a major issue.

This suggests that there are different theories about the role of variation in evolution, and indeed, there are.

Having different theories is not a bad thing. In a healthy scientific discipline, one expects different theories to compete with each other for success in prediction and explanation.

The problem is that this healthy sorting-out process isn't happening. The disconnects mentioned above go back generations. The problem is not that we haven't solved them already, but that we are not consciously and openly engaged in solving them. Rather than having a rigorous and decisive debate to resolve these and other troubling issues, we are bogged down in confusion.

The Wrong Turn

How did things get so muddled? I have a possible explanation. I don't expect you to believe my explanation just yet, because it depends on a lot of arguments that I have not presented yet. However, I need to present this historical hypothesis anyway to provide a context.

The main reason, in my opinion, that the process of science has gone so badly off track in evolutionary biology is the success of the Modern Synthesis.The main reason, in my opinion, that the process of science has gone so badly off track in evolutionary biology is the success of the Modern Synthesis. The Modern Synthesis was simultaneously both a reactionary theory of evolution- lets call it "Darwinism 2.0"- and a progressive socio-political campaign to establish Evolutionary Biology as a discipline with a unifying "modernist" narrative (a claim to subsume all relevant phenomena).

As a scientific theory, the Modern Synthesis replaced Darwin's fictional process of "fluctuating variation" with a verbal theory of the "gene pool". Like software engineers trying to re-design a popular application for a new operating system, the architects of the Modern Synthesis re-engineered the mechanistic "back end" of Darwinism to fit Mendelian genetics, but they left the "front end" the same, in order to preserve the familiar "look and feel" of Darwinism 1.0.2

The mechanistic secret to Darwinism 1.0 was variation on demand: "altered conditions of life" automatically turn on the flow of variation, producing abundant infinitesimal hereditary fluctuations precisely when (due to the "altered conditions of life") they would be leveraged by selection to build adaptation. Genetics refuted Darwin's theory of fluctuation (along with Lamarck's theory). The "gene pool" theory in Darwinism 2.0 held that Mendelian populations act as dynamic buffers of genetic diversity, so that abundant infinitesimal Mendelian variation is "soaked up like a sponge" and even "maintained", ensuring its constant availability. Thus, in Darwinism 2.0, the evolutionary engine comes with a tank full of fuel that automagically keeps itself full; in Darwinism 1.0, there is no storage tank, but fluctuating variation supplies fuel on demand, directly to the engine. Either way, the abundance of formless infinitesimal "raw materials" ensures that selection may spring into action to build anything, anywhere, anytime.

Though the "gene pool" idea was ingenious, no such reconciliation of Darwinism and genetics was necessary. A century ago, upon the discovery of genetics, scientists began moving rapidly toward a fresh and credible framework combining Mendelian genetics with reproductive sorting. While Darwin had rejected a role for "sports" or mutants on the grounds that they violated his principle of natura non facit salta (nature does not make leaps), early geneticists had no such doctrinal allegiances. With minor exceptions, they were ready to follow the evidence wherever it seemed to be leading, happily embracing dramatic saltations, and just as happily embracing tiny increments of change, depending on where the evidence seemed to point. They did not need to reconcile genetics with Darwinism, only with evolution.

But that was not enough for some. And that is when we took The Wrong Turn.

Within a generation, the leaders of the new discipline of Evolutionary Biology were all marching under a flag of unification—and there was no turning back. In hitching itself to Darwinism 2.0, the newly minted discipline of Evolutionary Biology had mortgaged its future to purchase the theoretical analog of a baroque castle. The proud new owners of this castle were not about to knock down any walls, much less to sell the place for something brighter and more open.

Science seeks consilience, and gets . . . muck

Science is driven by ingenuity, but its also driven by our aversion to cognitive dissonance. Uncovering and addressing "disconnects" or contradictions or paradoxes results in consilience, e.g., consilience between our intuitive verbal thinking, our mathematical theories, and our experimental results.

Surprises and contradictions invariably emerge in any discipline, and so this process of seeking consilience did not stop just because we underwent a mass conversion to monotheorism. The process continues, not by rejecting inadequate conceptual structures and building new ones, but by treating every challenge as a superficial problem that can be patched up with formless globs of conceptual mud- think of feckless notions like "constraints" or "contingency" or "molecular evolution". "Contingency" is a clumsy attempt to adapt a teleological and deterministic world-view to fit dynamic indeterminism.

The notion of "constraints", likewise, is a kludge to adapt an idealized view in which selection chooses from among all that is possible, to fit more closely to the reality that the process of variation renders some possibilities more likely than others. Ideally, we would have a theory that treats variation not as a static precondition, but as a process with kinetics that impose biases on the process of evolution. What we have instead is a concept of "constraint" that, if interpreted literally, is inadequate to cover all but the most extreme cases of variational effects (which typically are not rigid restrictions, but mere quantitative preferences), and if interpreted vaguely enough, can cover anything. Recasting the role of variation in terms of dynamic processes would require major renovations to the baroque castle, and who has time for that? Rather than developing a new view, we have opted for the vagueness and flexibility of "constraints".

Likewise, under healthier conditions, "molecular evolution" would have brought down the castle. Remarkably, in the 1970's, the same clique of influential thinkers (Mayr, Simpson, Dobzhansky, et al) were both 1) congratulating each other for having unified biology—not just evolution, but all of biology—in the Modern Synthesis (Mayr and Provine 1980), and 2) waging a deliberate campaign to convince biologists that results from molecular comparisons that seemed to fly in the face of this Modern Synthesis were not a direct challenge, because "molecular" and "organismal" represented different "levels" of organization with different metaphysical leverages, one for addressing ultimate "why" questions, and the other for mechanistic "how" questions (Dietrich 1998). Darwinism 2.0 survived due to our willingness to embrace a vapid new catechism: molecular evolution is different (but we still have one theory).

The "curious disconnect" is like a major rift or canyon, but its so full of mud that some pandits survey the state of evolutionary biology, and see only solid ground:

Any criticism of the synthetic theory that turned out to have some substance was subsumed in a modified version of this theory. Instead of being a weakness, this ability to change is one of the chief strengths of the synthetic theory of evolution" (Hull, 2002)

This is the process of reconciliation at work, and as you can see, sometimes the result is a steaming pile of offal.

Thus, the second premise of The Curious Disconnect is that, in the absence of a rigorous reconciliation of "disconnects", what we got instead is just a muddled, non-rigorous reconciliation. As this process continued decade after decade, we got bogged down in the muck.

The last "Synthesis" we'll ever need, or want?

Importantly, when I refer above to The Wrong Turn, I do not mean merely that a weak theory emerged with enthusiastic support. That might have been easy to fix-- by simply discarding the theory later-- had it not been for a more subtle shift by which we came to believe that our discipline required a single formalism to encompass everything we do and to provide all the answers to The Big Questions of evolution. We decided that, in order to be legitimate, we had to have an "ism".

One indication that we feel this way is that every few years, one of my colleagues notices that we've outgrown our ism, leaving some embarrassing bits exposed, and proposes to remedy this by calling for a "Newer" or "Extended" Synthesis, or calling on us to "finish" The Unfinished Synthesis. Not only do these proposals imply that 1) we used to have a comprehensive synthesis, and 2) such a synthesis continues to be possible and desirable, they also tend to suggest 3) the next synthesis really is here already, and just needs to be acknowledged.

I disagree with all of this, for reasons that I'll explain in subsequent posts.

For now, I just want to note that this doctrine of monotheorism is an anchor weighing us down. It sets an unachievable standard. It leads us to be embarrassed about the "disconnects" that we have, and to imagine that one new "synthesis" paper is going to set things right again, as though we already have agreed on a new set of answers and all it takes is for someone to state them out loud.

Contradictions, conflicts and "disconnects" are inevitable. The healthy approach to them is not to pretend that they don't exist, or shouldn't exist, but to confront them, beginning with the process of developing deep awareness.

So, I'm not going to propose another "synthesis". My primary goal is to raise awareness of problems and to achieve intellectual clarity, not to propose solutions. Once we are aware of the problems, we might all agree on the answers, but I doubt that the answers will be so obvious.

Whats ahead

This posting is just an introduction. I've tried to make three points. The first point is that there are deep "disconnects" or problems in the structure of evolutionary thought that have persisted for decades. Some of these diconnects relate to the role of variation in evolution.

The second point is that decades of attempts to rationalize conflicts and rescue decrepit doctrines and prop up the reputations of dead authorities have left us bogged down in confusion. This is not because the scientific issues are necessarily hard (though in some cases they are). Its because of the baggage we are carrying.

The third point is that a key part of this baggage is the belief that at every point in time all our work has to be subsumed by one great theory that is central to our identity as a discipline. I hope to convince you to reject this way of thinking. The realization that there are major problems to be solved ought to be exhilarating, not embarrassing. In my view, we should be starting a dialog, not calling for a resolution as though the problems were known and the answers were obvious.

So, when we wade into the "curious disconnect", we are going to be up our ears in muck that has accumulated for generations. But, we are not going to get bogged down, because we understand the nature of the problem and we aren't going to solve it all at once. We got into this mess primarily by a kind of shallow historical conservatism, preserving old doctrines and old ideas at the expense of conceptual rigor. To get out of this mess, we have to believe that, in science, its better to be clear than to be right. Our rule is going to be "if in doubt, toss it out". For instance, I truly believe that evolutionary theory would be better off if we all stopped invoking "random" and "constraint", immediately, today. "Random" is a constant source of confusion due to evolutionary biologists who are wedded to the doctrine "mutation is random" but who aren't committed to using a standard meaning of "random", and who simply devise a special definition to rescue this doctrine.

If that sort of muck-raking sounds interesting to you, I hope that you will follow The Curious Disconnect as it unfolds. Below is a list of whats coming up (in no particular order, and subject to change):

In a 4-part series, we'll explore The Mutationism Myth

We'll see how a simple verbal ambiguity can cloud our thinking in theory(I) vs. theory(II)

And we'll go further in this vein in Are there "mathematical" and "verbal" theories?

In Render unto Selection we'll practice some ways to make causal attributions when multiple causes are at work

Creativity and Gradualism will introduce the topic of Big Questions

Then, in The Big Questions, we'll consider the scope and explanatory power of evolutionary theories (and be humbled by the results)

In Mutation and Randomness (and other forms of domness), we'll learn how repeating a phrase will keep it alive even if no one knows what it means

Wednesday, March 17, 2010

This won't come as surprise to Canadians. We know that Canada gave Vietnam a pass. But Ann Coulter doesn't know this. (This is from 2006 but if Canadian Cynic can still use it make fun of the right-wing nutbars, then so can I.)

The one good thing about Ann Coulter is that she makes Sarah Palin look smart.

Evolutionary Imagery: Illustrating (and Distorting)the History of Life

Starts: Friday, March 19th 2010 at 7:00 pmEnds: Friday, March 19th 2010 at 9:00 pmLocation: Centre for Inquiry Ontario, 216 Beverley St., Toronto ON (just south of College St. at St. George St.)

Visual metaphors have been used to convey evolutionary ideas since Darwin's time. Some of the earliest kinds of images are still in use, even though they may do more to distort than to illustrate actual evolutionary processes. This seminar will explore two major evolutionary icons, the "Tree of Life" and "evolutionary line-ups", as they have been used in the past and how they must be interpreted today. Dr. T. Ryan Gregory completed his B.Sc. (Hons) at McMaster University in 1997 and earned his Ph.D. in evolutionary biology and zoology from the University of Guelph in 2002.

Jeffrey Shallit posted the questions for the 2010 Bernoulli Trials at the University of Waterloo (Waterloo, Ontario, Canada). This is a math contest for undergraduates. You have to decide whether each of following questions are true or false.

Professor Shallit liked the questions because one or two made him think for a bit. Bully for him! When I looked at the list I can honestly say that none of them (not a single one) made me think of anything except what is a Bernoulli and why is he doing this to undergraduates?

I wonder if I could made up questions like this for biology students? I don't think so—the choices would have to be "mostly true" and "mostly false."

This is my granddaughter Zoë celebrating her very first St. Patrick's Day.

Some of her Irish genes come from Jane's side of the family via my maternal grandparents. The shortest connection is to the parents of my grandmother. My great-grandfather was Thomas (Keys) Foster, born in County Tyrone on September 5, 1852. He immigrated to Canada in 1876. Thomas married Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. She immigrated to Canada in 1877.

Thomas and Eliza settled in Saskatchewan in 1883 and that's where my grandmother was born. Other ancestors in this line came from the adjacent counties of Donegal (surname Foster) and Fermanagh (surnames Keys, Emerson, Moore) and possibly Londonderry (surname Job).

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

Such natural structures exist. They are perfectly compatible with evolution. This prediction does not distinguish between Intelligent Design Creationism and real science.

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

The vast majority of of species with novel information have arisen gradually with plenty of transitional fossils to document their evolution. In a small number of cases (e.g. Cambrian Explosion) the evidence for evolution from known precursors is too sophisticated for creationists to follow. This prediction is not supported; therefore, Intelligent Design Creationism is falsified for all species where we have lots of data.

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

Convergence is perfectly consistent with evolution. This prediction is meaningless.

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

Most of our genome is junk. The evidence for this is overwhelming. Intelligent Design Creationism has been falsified.

That was easy.

In this regard, ID is falsifiable. When we test these predictions, ID passes those tests.

No it doesn't. Two of the "tests" are consistent with evolution so the "test" is meaningless. Intelligent Design Creationism fails the other two tests.

Some of you might not be regular readers of Panda's Thumb. If you're one of them, shame on you. Check it out to see what kind of an organism is shown in the photo. Is it animal, plant, fungus, protist, or bacterium?

Thursday, March 11, 2010

The Kitzmiller v. Dover trial took place in September/October 2005. The issue was whether Intelligent Design Creationism should be presented to Dover high school students as a valid scientific controversy [Kitzmiller v. Dover Area School District. The plaintiffs successfully argued that Intelligent Design was a religious view and as such it should be excluded from the science classroom.

The general thrust of the plaintiff's argument was laid out in the opening remarks of their lawyer (Eric Rothschild). They intended to show that science is restricted to natural causes. It cannot make statements about the supernatural. Since intelligent design refers to God it must be religion, not science, and should not be presented in a science classroom.

At this trial, you will hear the parties use the term "methodological naturalism." Methodological naturalism is the term used to describe science as self-imposed limitation, that it will only consider natural causes for natural phenomena. Science does not consider supernatural explanations because it has no way of observing, measuring, repeating, or testing supernatural events. It doesn't mean that supernatural events, including divine miracles, have not happened, just that science cannot properly make any statements about them.

But intelligent design will not accept the well-established boundaries of science and openly rejects methodological naturalism, the way science has been practiced for centuries. Why? Because it has to. In the end, no matter how many stones intelligent design throws at the theory of evolution, the only alternative it presents for the development and diversity of life, the only explanation for how a bacterial flagellum or the human eye came to be is a miracle, an abrupt appearance, an act of supernatural creation. That, by itself, establishes intelligent design as a religious argument, not a scientific argument, for the creation of biological life that cannot be taught to public school students.

This position is convenient because it defines non-overlapping magisteria. It means that someone can believe in miracles and supernatural beings without violating the principles that govern science. It's a good way of making the claims of intelligent design appear to be outside the bounds of science while, at the same time, allowing moderate religious scientists to live under the big tent of science.

It's a politically and legally effective tactic, but it it correct? I don't think it is. I think science is allowed to investigate claims of miracles and whether there are supernatural beings, just as it's allowed to investigate claims of the paranormal.

Expert testimony reveals that since the scientific revolution of the 16th and 17th centuries, science has been limited to the search for natural causes to explain natural phenomena. (9:19-22 (Haught); 5:25-29 (Pennock); 1:62 (Miller)). This revolution entailed the rejection of the appeal to authority, and by extension, revelation, in favor of empirical evidence. (5:28 (Pennock)). Since that time period, science has been a discipline in which testability, rather than any ecclesiastical authority or philosophical coherence, has been the measure of a scientific idea’s worth. (9:21-22 (Haught); 1:63 (Miller)). In deliberately omitting theological or “ultimate” explanations for the existence or characteristics of the natural world, science does not consider issues of “meaning” and “purpose” in the world. (9:21 (Haught); 1:64, 87 (Miller)). While supernatural explanations may be important and have merit, they are not part of science. (3:103 (Miller); 9:19-20 (Haught)). This self-imposed convention of science, which limits inquiry to testable, natural explanations about the natural world, is referred to by philosophers as “methodological naturalism” and is sometimes known as the scientific method. (5:23, 29-30 (Pennock)). Methodological naturalism is a “ground rule” of science today which requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify. (1:59-64, 2:41-43 (Miller); 5:8, 23-30 (Pennock)).

As the National Academy of Sciences (hereinafter “NAS”) was recognized by experts for both parties as the “most prestigious” scientific association in this country, we will accordingly cite to its opinion where appropriate. (1:94, 160-61 (Miller); 14:72 (Alters); 37:31 (Minnich)). NAS is in agreement that science is limited to empirical, observable and ultimately testable data: “Science is a particular way of knowing about the world. In science, explanations are restricted to those that can be inferred from the confirmable data – the results obtained through observations and experiments that can be substantiated by other scientists. Anything that can be observed or measured is amenable to scientific investigation. Explanations that cannot be based upon empirical evidence are not part of science.” (P-649 at 27).

This rigorous attachment to “natural” explanations is an essential attribute to science by definition and by convention. (1:63 (Miller); 5:29-31 (Pennock)). We are in agreement with Plaintiffs’ lead expert Dr. Miller, that from a practical perspective, attributing unsolved problems about nature to causes and forces that lie outside the natural world is a “science stopper.” (3:14-15 (Miller)). As Dr. Miller explained, once you attribute a cause to an untestable supernatural force, a proposition that cannot be disproven, there is no reason to continue seeking natural explanations as we have our answer.

One of the people who testified for the plaintiffs was John Haught, a Roman Catholic Theologian. He was asked to define science and distinguish it from religion. His testimony is a very good example of the accommodationist position so I'm quoting it below in order to illustrate that view. (The transcripts are freely available on the NCSE website, see Kitzmiller Trial Transcripts.)

Q. Focusing on natural science, what is science?
A. Science is a mode of inquiry that looks to understand natural phenomena by looking for their natural causes, efficient and material causes. It does this by first gathering data observationally or empirically. Then it organizes this data into the form of hypotheses or theories. And then, thirdly, it continually tests the authenticity of these hypotheses and theories against new data that might come in and perhaps occasionally bring about the revision of the hypothesis or theory.

Q. You said that science seeks to understand the natural world through natural explanations. Is that important?
A. Yes, that's critical. The science, by definition, limits itself self-consciously, methodologically, to natural explanations. And that means that anything like a supernatural reality or transcendent reality, science is simply not wired to pick up any signals of it, and therefore any reference to the supernatural simply cannot be part of scientific discourse. And this is the way that science carries on to our present day.

Q. Would that mean this is the way modern science is conducted?
A. Modern science we date from roughly the end of the 16th to the 17th Century, in that period of time. And it was at that time that the great figurists of modern science, almost all of whom were deeply religious men themselves, decided self-consciously that this new mode of inquiry would not appeal to anything that's not natural, would not appeal to things like value, importance, divine causation, or even anything like intelligent causation.

These are not scientific categories of explanation. And ever since the 16th and 17th Century, modern science, as it's called, leaves out anything that has to do with theological or ultimate explanation.

....

Q. Does this make science at odds with religion?
A. By no means. Science and religion, as I've written in all of my books, are dealing with two completely different or distinct realms. They can be related, science and religion, but, first of all, they have to be distinguished. The medieval philosopher said, we distinguish in order to relate. And when we have a failure to distinguish science from religion, then confusion will follow.

So science deals with questions relating to natural causes, to efficient and material causes, if you want to use Aristotelian language. Religion and theology deal with questions about ultimate meaning and ultimate purpose. To put it very simply, science deals with causes, religion deals with meanings. Science asks "how" questions, religion asks "why" questions.

And it's because they're doing different things that they cannot logically stand in a competitive relationship with each other any more than, say, a baseball game or a baseball player or a good move in baseball can conflict with a good move in chess. They're different games, if you want to use that analogy, playing by different rules.

Q. You've used another analogy in discussions with me that might be illuminating. This is the boiling water analogy. Could you give us that?
A. Yes. I think most of the issues in science and religion discussions, most of the confusion that occurs happens because we fail to distinguish different levels of explanation. And so what I advocate is layered or -- layered explanation or explanatory pluralism, according to which almost every phenomenon in our experience can be explained at a plurality of levels.

And a simple example would be a teapot. Suppose a teapot is boiling on your stove and someone comes into the room and says, explain to me why that's boiling. Well, one explanation would be it's boiling because the water molecules are moving around excitedly and the liquid state is being transformed into gas.

But at the same time you could just as easily have answered that question by saying, it's boiling because my wife turned the gas on. Or you could also answer that same question by saying it's boiling because I want tea.

All three answers are right, but they don't conflict with each other because they're working at different levels. Science works at one level of investigation, religion at another. And it would be a mistake to say that the teapot is boiling because I turned the gas on rather than because the molecules are moving around. It would be a mistake to say the teapot is boiling because of molecular movement rather than because I want tea. No, you can have a plurality of levels of explanation. But the problems occur when one assumes that there's only one level.

And if I could apply this analogy to the present case, it seems to me that the intelligent design proponents are assuming that there's only one authoritative level of inquiry, namely the scientific, which is, of course, a very authoritative way of looking at things. And they're trying to ram their ultimate kind of explanation, intelligent design, into that level of explanation, which is culturally very authoritative today, namely the scientific.

And for that reason, science, scientists justifiably object because implicitly they're accepting what I'm calling this explanatory pluralism or layered explanation where you don't bring in "I want tea" while you're studying the molecular movement in the kettle. So it's a logical confusion that we have going here.

I think that's a prety good description of the accommodationist position as I understand it.

One of the interesting aspects of the trial is that when John Haught started to testify as an expect on science there was an objection from the defendant's lawyer. He claimed that Haught was a philosopher, not a scientist, and therefore was not an expert witness with respect to defining science. The objection had to be withdrawn when the defendant's lawyer discovered that he had already approved pre-trial documents where Haught discussed science.

Later on there was the following exchange,

Q. Well, according to Gould, the message of Darwinian science is that life has no purpose. Is that a scientific claim?
A. No. And I think if you ask Gould, he would have to admit that, also.

Q. Okay. Daniel Dennett, do you know who he is?
A. Yes.

Q. He's a philosopher. Is that right?
A. He's a philosopher at Tufts University.

Q. Right. And he claims that Darwin is incompatible with religious beliefs?
A. Yes. He's a philosopher, not a scientist. That's a philosophical belief.

Q. Well, what about E. O. Wilson, who is a biologist at Harvard, he puts Darwin's science in direct competition with religion, does he not?
A. Yes, because he is one of these people who unconsciously conflates his very good evolutionary science with a very suspect metaphysical belief system. Not always, but at times.

I'm sorry, but I can't help but snicker at such testimony from a Roman Catholic philosopher. He's testifying as an expert on science but criticizes another philosopher for making statements about science (justifiable, in my opinion, but still hypocritical). Then he criticizes a scientist for mixing up his science with his metaphysical beliefs.

What, exactly are those "very suspect metaphysical belief system" that John Haught avoids but which entraps E.O. Wilson? Why it's the "religion" of materialism.

Q. And by a materialist world-view or belief system, what does that mean?
A. Materialism is a belief system that claims that matter, lifeless and mindless matter, is the ultimate foundation of all reality, and there's nothing more ultimate than that. So it's kind of religious in the first sense of my term, a belief in something of ultimate importance. For the materialist, matter is the ultimate creator, the ultimate source of all being, and therefore it excludes the existence of anything supernatural, certainly the existence of God.

So, materialism isn't something that could just arise by default among those people who don't fall for religion. No siree. It has to be a religious view of its own.

If you think about it, that's very strange. Western Europeans are raising a whole generation of children who will have never been brainwashed by religion. They will be materialists by default because they've never known anything else. But according to Haught (he's not alone) they will be engaging in adopting a form of religious belief system, just like E.O. Wilson. How does that work?

So, what exactly are the limitations of science that we are supposed to adhere to? Earlier I criticized the concept of methodological naturalism because it seemed to rule out investigations of the paranormal as well as investigations of miracles. Robert Pennock, another philosopher, was asked about that during his testimony and he had a ready answer. See if you are convinced.

Q. Isn't it true that as we sit here today scientists are investigating what some people call psychic powers?
A. I know that there are a few scientists who did that I believe. Mack is one name, someone who's done this. So there are a few scientists who have done that, that's right, and what they do in that case is really the same thing. It's often misunderstood to think, to call something paranormal means that it is supernatural. Essentially what's going on in those scientific investigations is to say no, that's not so. We will again treat this purported phenomenon, ESP or telekinesis for example, as though this is a natural, still yet unknown, but ordinary causal process, treating it essentially in the same way we treat other things under the constraints of methodological naturalism, reconceptualizing it as a natural thing rather than a supernatural.

Cool. You can investigate the paranormal because it's not supernatural and you can treat it as a potential natural phenomenon. Presumably you will reach the conclusion that is is not a paranormal event.

But for some reason you can't do that for miracles and the role of God in theistic evolution. That's forbidden science.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.